SURE-tools 2.4.17__py3-none-any.whl → 2.4.32__py3-none-any.whl

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Files changed (12) hide show
  1. SURE/DensityFlow.py +85 -68
  2. SURE/DensityFlow2.py +1422 -0
  3. SURE/DensityFlowLinear.py +1413 -0
  4. SURE/PerturbationAwareDecoder.py +737 -0
  5. SURE/VirtualCellDecoder.py +0 -1
  6. SURE/__init__.py +7 -2
  7. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/METADATA +1 -1
  8. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/RECORD +12 -9
  9. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/WHEEL +0 -0
  10. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/entry_points.txt +0 -0
  11. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/licenses/LICENSE +0 -0
  12. {sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/top_level.txt +0 -0
SURE/VirtualCellDecoder.py CHANGED
@@ -56,7 +56,6 @@ class VirtualCellDecoder:
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  print(f" - Biological Prior Dimension: {biological_prior_dim}")
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  print(f" - Device: {self.device}")
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  print(f" - Parameters: {sum(p.numel() for p in self.model.parameters()):,}")
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- print(f" - Estimated GPU Memory: ~8-10GB (optimized for 20GB)")
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  class BiologicalPriorNetwork(nn.Module):
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  """Biological prior network based on gene regulatory knowledge"""
SURE/__init__.py CHANGED
@@ -1,15 +1,18 @@
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  from .SURE import SURE
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  from .DensityFlow import DensityFlow
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+ from .DensityFlowLinear import DensityFlowLinear
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  from .PerturbE import PerturbE
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  from .TranscriptomeDecoder import TranscriptomeDecoder
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  from .SimpleTranscriptomeDecoder import SimpleTranscriptomeDecoder
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  from .EfficientTranscriptomeDecoder import EfficientTranscriptomeDecoder
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  from .VirtualCellDecoder import VirtualCellDecoder
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+ from .PerturbationAwareDecoder import PerturbationAwareDecoder
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  from . import utils
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  from . import codebook
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  from . import SURE
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  from . import DensityFlow
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+ from . import DensityFlowLinear
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  from . import atac
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  from . import flow
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  from . import perturb
@@ -18,6 +21,8 @@ from . import TranscriptomeDecoder
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  from . import SimpleTranscriptomeDecoder
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  from . import EfficientTranscriptomeDecoder
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  from . import VirtualCellDecoder
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+ from . import PerturbationAwareDecoder
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- __all__ = ['SURE', 'DensityFlow', 'PerturbE', 'TranscriptomeDecoder', 'SimpleTranscriptomeDecoder',
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- 'EfficientTranscriptomeDecoder', 'VirtualCellDecoder', 'flow', 'perturb', 'atac', 'utils', 'codebook']
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+ __all__ = ['SURE', 'DensityFlow', 'DensityFlowLinear', 'PerturbE', 'TranscriptomeDecoder', 'SimpleTranscriptomeDecoder',
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+ 'EfficientTranscriptomeDecoder', 'VirtualCellDecoder', 'PerturbationAwareDecoder',
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+ 'flow', 'perturb', 'atac', 'utils', 'codebook']
{sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.4.17
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+ Version: 2.4.32
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.4.17.dist-info → sure_tools-2.4.32.dist-info}/RECORD RENAMED
@@ -1,11 +1,14 @@
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- SURE/DensityFlow.py,sha256=YvaE9aPbAC2U7WhTye5i2AMtcw0BI_qS3gv9SP4aE0k,56676
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+ SURE/DensityFlow.py,sha256=M8yDMCzH-LSVjFB34pUaN2TNUqo0jnZMmaFcLLjtYBU,57218
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+ SURE/DensityFlow2.py,sha256=BBRCoA4NpU4EjghToOvowo17UtwYokTN75KxWYHTX1E,58404
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+ SURE/DensityFlowLinear.py,sha256=RfjIwXxO0gWQni7LHRy4DSDUkdz3HpDjlZbxJse65Ts,57515
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  SURE/EfficientTranscriptomeDecoder.py,sha256=O_x-4edKBU5OJJbOOS-59u3TQElZqhAtOVJMPlpw8m0,21667
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  SURE/PerturbE.py,sha256=DxEp-qef--x8-GMZdPfBf8ts8UDDc34h2P5AnpqZ-YM,52265
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+ SURE/PerturbationAwareDecoder.py,sha256=duhvBvZjOpAk7c2YTfmA2qKbrgVvwT7IW1pxaukq_iU,30231
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  SURE/SURE.py,sha256=MXs7iuvcj-lU4dJ_MwKegpL2Rqk2HB4eFfAgHRA3RtA,47744
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  SURE/SimpleTranscriptomeDecoder.py,sha256=mLgYYipfRrmuXlpoaxLPfJS009OVwyshdL3nXTJygIE,22285
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  SURE/TranscriptomeDecoder.py,sha256=n2tVB8hNVLwSQ1G1Jpd6WzMl2Iw63eK0_Ujk9d48SJY,20982
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- SURE/VirtualCellDecoder.py,sha256=X37TbiddREugON10Y9TJ2M-UzrRKe2o185d2-6FtW_M,27542
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- SURE/__init__.py,sha256=ZHatQR813LVibrHOLkemTXFt3eSpyluWGxAi8doQTD4,879
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+ SURE/VirtualCellDecoder.py,sha256=z1Z7GRTYmTE3DaSKZueofv138R0J7kGFfnh0a_Lee38,27468
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+ SURE/__init__.py,sha256=ayUV9hNysHtZxbRK87nnC6cXs-7wAq6FUkllqotrx8E,1123
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  SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
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  SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
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  SURE/assembly/atlas.py,sha256=ALjmVWutm_tOHTcT1aqOxmuCEQw-XzrtDoMCV_8oXLk,21794
@@ -22,9 +25,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
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  SURE/utils/custom_mlp.py,sha256=Rn_PQouxPMSda-KKBYrwVVv3GFFuUmCLxp8cV5LszZo,10580
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  SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
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  SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
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- sure_tools-2.4.17.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
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- sure_tools-2.4.17.dist-info/METADATA,sha256=Qv8OlzL7iQmfG1pGSdSQG-uo92pVRFHJTvMASWxdwwo,2678
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- sure_tools-2.4.17.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- sure_tools-2.4.17.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
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- sure_tools-2.4.17.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
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- sure_tools-2.4.17.dist-info/RECORD,,
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+ sure_tools-2.4.32.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
29
+ sure_tools-2.4.32.dist-info/METADATA,sha256=9o2WcDEY2JIf1AhclsLePndrjYVexLj9QUHtZjzGc38,2678
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+ sure_tools-2.4.32.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ sure_tools-2.4.32.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
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+ sure_tools-2.4.32.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
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+ sure_tools-2.4.32.dist-info/RECORD,,